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  • heterozygosity and allele balance in NGS doubt

    Hi,

    I have data from a target enrichment on a few human genes, of course sequenced through NGS. Enrichment, sequencing and data analysis were performed by a private genomic service.

    In the VCF file some variants show an allele frequency around 1-2%, but their locus is called as heterozygous. Isn't the variant presence too low to call it as heterozygous?

    I am not too acquainted with these kind of analysis, so I am a little confused by this. Could someone please help me out?

    Thanks a lot in advance.

    Marco

  • #2
    Why not do some filtering on the data ? Think vcfutils will do this for you.

    Generally people might take variants with an allele frequency cutoff of around 22% to be genuine heterozygotes. Sometimes you get a nice 50/50 ratio, but you miss out on a lot of data if you stick to very strict thresholds.

    Certainly reporting 1-2% AF as heterozygotes is not great analysis.

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